Fig. 5

TCR diversities in JIA. A Box plots showing the alpha diversities of TCR α and β in healthy control and JIA groups. The y-axis indicates alpha diversity representing the clonotypic diversity of specific TCR locus. Green and red dots indicate samples of healthy controls and JIA patients, respectively. Asterisks denote the significance levels of differences between the clonotypic diversities of TCRs within healthy controls and that within JIA patients. *, P < 0.05; **, P < 0.01; ***, P < 0.001. B A Uniform Manifold Approximation and Projection (UMAP) plot of 67,235 T cells from seven JIA patients showing 16 major clusters (nine for 34,605 CD4⁺ and seven for 32,630 CD8⁺ T cells). Each dot represents an individual T cell and color indicates cluster origin. C Left. A bar plot showing the number of single T cells and frequencies of unique and expanded T cell clones in each cluster. The inset numbers indicate the proportion of the cell type in the cluster. Right. UMAP plot showing the clusters with the clone types. The colors correspond to the number of clones (i.e. clonal abundance). D A scatter plot showing the alpha diversity of TCR in each cluster. The red and blue colors denote CD4⁺ and CD8⁺ T cells, respectively. E Module enrichment analysis between expression levels of scRNA-seq CD4_C5 cluster and black co-expression gene set derived from JIA case-control expression data (GSE13501). The gene list of the black modules is in Table  S9.